Disagreement of results with samtools and bedtools about mosdepth HOT 7 CLOSED

there are several other issues related to this. mosdepth does not double-count overlapping bases. bedtools does (I assume IGV does as well). For every issue like this one that has provided data, I have checked and never found a bug in mosdepth.

mosdepth will often have lower depth than bedtools because bedtools double-counts overlapping bases--it may also use different include/exclude flags

mosdepth will often have a higher depth than samtools depth, but samtools depth and samtools mpileup often do not agree even for identical parameters.

from mosdepth.

Can we run mosdepth to double-count overlapping bases ?

from mosdepth.

the next-release of mosdepth will have a mode that does not correct for mate-overlap.

from mosdepth.

That would be really great. How soon can we expect this release ?

from mosdepth.

The new release is out with --fast-mode that will not correct for overlapping mates.

from mosdepth.

I am a lillte confused, but I am sure you are right.
the accumlated depth is because of reads overlap, so here does not take overlap means the overlap will be calculated as many times as overlaped reads multiply 2 ?

from mosdepth.

this is only relevant when a read-pair from the same fragment (with same read-id) overlaps.

from mosdepth.